The Latest GTN News

Keep an eye on this page for the latest news around the GTN. New tutorials, GTN features, upcoming training events, and much much more!

Want to add your own news here (e.g. new tutorial, event, publication, anything else training related)? Check out how to do that in this FAQ

four graphs showing increases over time: training materials including slides and tutorials; contributors; workflows; and other

GTN's Gift for 2024

19 December 2024

Community Pages

gtn single-cell new feature new tutorial contributing community

A group of people standing along a staircase holding up the Vulcan salute for SPOC: 'Live long and prosper'. They look relatively happy. Taken at 2024 Galaxy Community Conference.

🖖🏾Galaxy SPOC Community: Year in Review

18 December 2024

🚀 2024: A SPOC-tacular Year in Review 🌌

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Organizing GTA2025: Give us feedback and your availability!

17 December 2024

Give us feedback and your availability for the GTA 2025

gtn event teaching contributing community

swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)

SPOC CoFest 2024: How did it go?

6 December 2024

First SPOC CoFest

gtn single-cell

A screenshot of the GTN's short introduction to Galaxy tutorial. There are two authors and two editors, but now shown is a new reviewers with 13 individuals, some overlapping with editors and authors.

Credit where it's due: GTN Reviewers in the spotlight

2 December 2024

We would like to recognise and thank all of the reviewers who have contributed to the GTN tutorials; your efforts are greatly appreciated, and we are grateful for your contributions to the GTN community. Today, we are highlighting your efforts on every single learning material across the GTN.

gtn infrastructure new feature automation contributing community

Analysis Pipeline for Tracking Mitochonria and Capturing Mitoflashes.

New Tutorial: Tracking of mitochondria and capturing mitoflashes

29 November 2024

We are happy to share that a new imaging tutorial for Tracking Mitochondria and Capturing Mitoflashes is now available in the Galaxy Training Network!

bioimaging mitoflash mitochondria imaging

One of the many charts from the report. Histogram of the average duration, in hours, an upgrade takes (excluding DB schema migration). Showing a median of 3 and mean of 4. Mostly under 3, but a few values around 7.

Galaxy Administrator Time Burden and Technology Usage

22 July 2024

Have you wondered how difficult Galaxy is to run? How much time people must spend to run Galaxy? In February 2024, we collected 9 responses from the Galaxy Small Scale Admin group. The questions cover various time burdens and technological choices. The report provides answers to prospective future admins’ most common questions.

deploying maintenance survey admin

A screenshot of the GTN Google Form for news contributions. The form is titled 'GTN News' and has fields for 'Title', with a screenshot of a galaxy single cell news post as the header image.

Simplifying GTN contribution with Google Forms

17 July 2024

Since the last time we announced GTN news posting via Google Form, we’ve found that this has been an excellent fit for the community and decided to greatly expand the use of Google Forms for GTN contributions.

gtn infrastructure new feature automation contributing

Analysis Pipeline with SnapATAC2

New Tutorial: Single-cell ATAC-seq standard processing with SnapATAC2

12 July 2024

We are proud to announce that a new training, explaining the analysis of single cell ATAC-seq data with SnapATAC2 and Scanpy, is now available in the Galaxy Training Network.

new tutorial single-cell epigenetics

Registration Open for BioNT Community Event & CarpentryConnect Heidelberg

11 July 2024

Are you interested in training and want to connect with other enthusiastic trainers? Then join the BioNT Community Event & CarpentryConnect - Heidelberg 2024. The Carpentries and other learning communities will meet to network and collaborate during this 3-day event. The GTN will be present with a Poster, Lightning Talks and a Mini-hackathon.

So many new features! GTN 2023-2024 Updates

9 July 2024

We recently presented the GTN at the 2024 Galaxy Community Conference. This presentation was a summary of the updates and new features that were added to the GTN in the past year.

gcc gtn infrastructure contributing

banner image for the mTB training event showing the name of the course over a background of a touchscreen showing data

4th Mycobacterium tuberculosis complex NGS made easy

8 July 2024

Tuberculosis (TB) is a big killer in many countries of the world, particularly in those with low and middle income. Next-generation sequencing has been key in improving our understanding of drug resistance acquisition and of transmission of Mycobacterium tuberculosis. Yet, the need for expertise guiding NGS implementation in laboratories and the lack of bioinformatic expertise, are main obstacles hindering the implementation of NGS into TB programs.

NGS Tuberculosis Drug-resistance transmission evolution one-health microbiome

Screenshot of the GTN Video Library showing a tutorial recording with a large youtube player and extensive metadata about who created the video (Natalie Kucher) and when, how long, etc.

GTN Video Library 2.0: 107 hours of learning across 154 videos

14 June 2024

Many GTN tutorials already have recordings. These recordings were made by members of the community for a variety of (online) training events. Up until now, this video library were part of the Gallantries Project. We have now integrated this video library directly into the GTN, and made it even easier to add video recordings to GTN tutorials or slide decks! Just use a Google Form to submit your video recordings!

gtn contributing teaching community

Hand drawn sketch of a phylogenetic tree from Charles Darwin's notebook

Phylogenetics tutorial takes researchers back to basics!

13 June 2024

A new Galaxy Training Network tutorial has been created to take researchers back to basics to uncover the principles of phylogenetics and how tree-building methods work. A longstanding collaboration between Professor Michael Charleston from the University of Tasmania and Australian BioCommons has delivered this self-guided tutorial featuring videos and hands-on exercises. To maximise its impact, the resource was tailored specifically to be shared globally via the Galaxy Training Network, and will form the basis of an upcoming live training workshop.

Phylogenetics Tutorial GTN Australian BioCommons evolution

From GTN Intern to Tutorial Author to Bioinformatician

13 June 2024

With growing access and interest in sequencing data, Galaxy is a knight in shining armor for wet lab scientists hoping to analyze their own data. With long term intentions of increasing access to bioinformatic analyses, the Galaxy Training Network (GTN) creates a safe space where non-computer-scientists may analyze their own data and even learn to code: an invaluable skill in today’s scientific world. Galaxy introduced me to brand new skills as an undergraduate and ultimately changed the trajectory of my career. Here is my story as a biology undergraduate with no coding experience turned GTN contributor &, eventually, coding bioinformatician: thanks to Galaxy.

single-cell training education trajectory user contributor contributing

Open Call for Trainers for the Galaxy Training Academy

11 June 2024

We are happy to announce the Galaxy Training Academy 2024, a global online training event, where learners can get to know Galaxy and learn how to analyze data for various research topics.

gtn teaching contributing

New Galaxy training: Building an amplicon sequence variant (ASV) table from 16S data using DADA2

6 June 2024

The GTN hosts its 400th tutorial: Building an amplicon sequence variant (ASV) table from 16S data using DADA2

new tutorial microbiome

400 tutorials

Celebrating the Milestone: 400 Tutorials on the Galaxy Training Network!

6 June 2024

The Galaxy Training Network (GTN) has reached an exciting milestone: our 400th tutorial! This achievement is a testament to the dedication and hard work of our community of educators, researchers, and developers over the last 9 years.

gtn contributing community

section in the Galaxy Tool Form titled 'Tutorials' listing all 13 GTN tutorials which use the cat tool

Integrating the Galaxy Training Network into the Tool Form

4 June 2024

For many tools in Galaxy, the GTN offers a variety of guides, practical examples, and help throughout it’s many tutorials. Often times when using a tool, such information can be very useful, but hard to discover.

gtn new feature contributing

Standards compliant™ training news via RSS/Atom

4 June 2024

gtn infrastructure contributing

screenshot of galaxy data upload interface showing a folder named GTN Training Data

All GTN training data are now automatically mirrored via Onedata

3 June 2024

As part of the EuroScienceGateway and in cooperation with Onedata and EGI we are providing all GTN training data on a publicly accessible cloud storage. Those training datasets are curated, small but meaningful for educational purposes and contain 1530 files with a total size of 170Gb. An invaluable set of resources for everyone dealing with data science and training. Please thank the more than 350 contributors to GTN.

esg-wp4 esg contributing

A screenshot of a GTN event page showing the program tab. It looks very similar to GTN topic pages.

Introducing GTN Event Pages

22 May 2024

Are you organizing a training event using GTN materials? You can now add your event directly to the GTN!

gtn infrastructure new feature events contributing community

Open Galaxy Position at Galaxy Europe Team, University of Freiburg

15 May 2024

jobs freiburg eu

A screenshot of a radar plot visibly from fair-checker's site showing a perfect score.

Perfectly FAIR Training!

13 May 2024

We are happy to report that over the years of our fruitful collaboration with ELIXIR TeSS, all GTN materials should receive a perfect score on the FAIR-Checker.

gtn infrastructure fair contributing

Open Galaxy Positions at Melbourne Bioinformatics

24 April 2024

Melbourne Bioinformatics is expanding their team and recruiting three new roles to work on bioinformatics training, outreach, and research.

jobs australia

A screenshot of the MINERVA Platform's COVID-19 Disease Map showing the PAMP signalling pathway submap in view in center as well as some genes in a table to the right.

Learn to use MINERVA Platform's COVID-19 Disease Map with Galaxy

28 March 2024

As part of the work of BeYond COVID, we have developed a new integration between the MINERVA Platform’s COVID-19 Disease Map and Galaxy! Datasets created within Galaxy can now be seamlessly visualized in the MINERVA Platform, allowing you to explore your data in the context of the COVID-19 Disease Map.

by-covid pathways minerva gtn infrastructure new feature one-health transcriptomics

FAIR TRaining Learning Pathway By ELIXIR fellows funded by the ELIXIR UK DASH project

New Learning Pathway for FAIR Data Management developed by ELIXIR-UK Data Stewardship Fellows and Experts

26 March 2024

ELIXIR-UK’s Data Stewardship Fellowship is excited to announce a new learning pathway focused on FAIR Data Management! This program equips researchers and research support staff with the skills to effectively manage their research data.

fair dmp data stewardship data management new learning pathway

Cool URLs Don't Change, GTN URLs don't either.

18 March 2024

At the Galaxy Training Network we are really committed to ensuring our training materials are Findable, Accessible, Interoperable, and Reusable. This means that we want to make sure that the URLs to our training materials are persistent and don’t change. The GTN wants you to be able to rely on our URLs once you’ve added them to a poster or training material, without having to worry about them breaking in the future.

gtn infrastructure new feature contributing

Lost in a topic? Try a Learning Pathway!

4 March 2024

We know the GTN has a lot of learning materials (400 and counting!) which can make it quite difficult to figure out where to start in some topics.

gtn infrastructure new feature

GTN ❤️ GMOD

29 February 2024

Building upon the work previously done for the SARS-Cov-2 Topic we have further expanded the ‘tag based topics’ to support a new GMOD topic.

new topic new feature genome-annotation GMOD

cropped picture of a mobile phone interface showing a terminal with Galaxy log outputs.

🪐📲 Hosting Galaxy at the Edge: Directly in Your Pocket!

31 January 2024

Hey Galaxy admins! Have you ever wanted to administer your own instance from the luxury of your pocket?

fun system administrators developers humour admin

GTN in Discourse

30 January 2024

Howdy teachers and support staff! We are exploring displaying GTN content directly in the Galaxy Help site, furthering the integration between the GTN and the Galaxy community infrastructure. When you paste a GTN Frequently Asked Questions URL into the Galaxy Discourse, it will now be rendered directly in Discourse!

contributing community

Simplified GTN News submission via Google Form

29 January 2024

Based on user feedback of the difficulties of the GTN news submission process we have significantly simplified and removed the need for manually editing a YAML file by providing a quick and easy Google Form

contributing community

FAIR Data management in single cell analysis

17 January 2024

New single cell section: Changing data formats & preparing objects

single-cell data management data import fair

swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)

Galaxy Single-cell Community: Year in Review

22 December 2023

🚀Embarking on a cosmic journey, the Galaxy Single-cell Community has clustered together to unveil a constellation of tools, making strides in RNA-stellar discoveries and creating out-of-this-world workflows. With a commitment to battling work duplication across the multiverse, this community is boldly charting a course for global domination, proving that when it comes to bioinformatics, the Galaxy is the limit!✨

gtn communications single-cell

GTN Helper Bots Connect the Galaxy

20 December 2023

🤖💬 Bleep bloop! Good news everyone! We have deployed some bots to enable our Matrix regulars to better engage with the contributions and questions of our users on the non-Matrix side of the Galaxy-verse.

gtn communications contributing

User story: Where Galaxy meets medicinal chemistry

18 December 2023

As a medicinal chemistry student, I undertook a semester project on natural products isolation and derivatisation. One of the compounds my group was working on was piperine, extracted from black pepper. Inspired by literature findings, we found out that the derivatives of piperine can inhibit monoamine oxidase-B and thus can be possibly used in Parkinson’s disease. As a novelty element in our project, we came up with new structures of derivatives that could act as inhibitors.

computational-chemistry user story gtn

Tutorial Feature: Easier launching of WorkflowHub & Dockstore Workflows

12 December 2023

While most GTN tutorials include their associated workflow directly in the GTN, some may wish to write a tutorial about running workflows from WorkflowHub, e.g. leveraging the IWC workflow collection.

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Feedback: Easy slide recordings

21 November 2023

I recently imported Friends Don’t Let Friends Make Bad Graphs, a fantastic and educational github repository showcasing some common visualisation mistakes, that was available under an open license, to the GTN. Then the GTN automatically made a video for me.

feedback testimonial gtn contributing

GTN has left Twitter/X as of October

21 November 2023

We did not formally announce it at the time, but the Galaxy Training Network has migrated from Twitter/X to Mastodon, as that platform no longer aligns with the Galaxy Project Code of Conduct nor our community values.

gtn communications contributing

Update: Workflow List now searches WorkflowHub.eu, advanced query syntax

20 November 2023

feature update gtn contributing

Single cell subdomain re-launch: Unified and feedback-driven

12 October 2023

The European Galaxy Days 2023 CoFest combined the forces of administrator, developer and trainer to update and re-launch the single cell Galaxy instance. Where previously there were two subdomains each with their own sets of tools, there is now a unified subdomain with re-categorized tools that makes sense for users.

gtn single-cell

New Feature: Embeddable GTN Tutorial Lists and UseGalaxy Workflow List Widgets

5 October 2023

We at the GTN strive to bring you the most fun and fancy features we can in a completely static site! Today we’re addressing the question of Wendi Bacon who needed a solution for keeping her single cell subdomain up-to-date with all the latest happenings in the Single Cell world.

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New Feature: GTN User Preferences

20 July 2023

We have added a new “User Preferences” page for our GTN users! This gives you more control over both how the GTN looks, and works, for you.

new feature gtn contributing

AI4Life teams up with GTN to enhance training resources

27 June 2023

This is an external post, please follow the link to read it.

new topic new community imaging

ELIXIR-UK Fellow Launches New FAIR Data Management Training

21 June 2023

Katarzyna Kamieniecka (University of Bradford), a member of the ELIXIR-UK Fellowship Programme, has just launched a new series of lessons to improve {FAIR} data management in the life sciences. The lessons are designed to help researchers and research support staff understand the principles of FAIR data management and apply them to their own work.

new topic new tutorial fair

New Feature: Pan-Galactic Tool Search

7 June 2023

Did you ever want to run a tool, but not know where it might be available? The GTN has you covered with the Pan-Galactic Tool Search that is now available.

new feature gtn contributing

GTN Celebrates Pride Month: Alan Hart & M. Tuberculosis

1 June 2023

June is Pride Month in the US and countries around the world. We have automatically activated the new Progress Pride theme on the home page (Click to Activate) if you hadn’t already selected a theme.

contributing

Schematic of an isoform switch and detection pipeline. Data is annotated and a prediction is made for isoform switch consequences

New Galaxy training: Genome-wide alternative splicing analysis

15 May 2023

The GTN hosts a new training for analyzing alternative splicing at genome-wide scale!

new tutorial transcriptomics

BY-COVID and RO-Crate collaboration brings new topic: FAIR Data, Workflows & More

11 May 2023

As part of the BY-COVID project, the RO-Crate team and BY-COVID members have brought several RO-Crate related tutorials into the Galaxy Training Network, under a brand new {FAIR} topic!

new topic new feature fair

New Feature: my.galaxy.training

20 April 2023

The GTN has set up a very simple “redirection” service based on my.home-assistant.io which Helena discovered after reading some Home Assistant documentation and saw a really neat link which led to her own internal home assistant.

new feature gtn contributing

the bottom left corner of an overview box from a training material is shown, a label short link clearly has a short link as described in the tutorial

New Feature: Persistent URLs (PURLs) / Shortlinks

19 April 2023

The GTN has added persistent URL identifiers for our tutorials, slides, and FAQs. Using the gxy.io service, we have reserved GTN namespace for our persistent URLs. These work similarly to DOIs in that they will always point to a specific training material.

new feature gtn contributing

New Feature: GTN Rdoc

19 April 2023

The internal functions of the GTN have, in the past, not been very well documented. Now we have started the process of fully documenting the functions and modules available to GTN developers.

new feature gtn contributing

New Feature: Click-to-run Workflows

19 April 2023

The GTN has implemented “click to run” workflows! One click, will get you into Galaxy with a workflow imported and ready to run. If you are on either usegalaxy.org or usegalaxy.eu, we have implemented easy buttons which you can click that will direct you straight to your Galaxy server.

new feature gtn contributing

a graphic depicting a winding path from a start symbol to a trophy, with tutorials along the way

New Feature: Learning Pathways!

13 April 2023

Introducing Learning Pathways in the GTN! Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge step by step.

new feature contributing

New Feature: Trainer Directory! (Add yourself today!)

21 March 2023

Numerous other training groups keep “Trainer Directories” as a way to help students meet trainers in their area, especially for hosting workshops for their local community. There have been a handful of attempts at this in the past, both in galaxyproject/galaxy-maps and in a Google Map on the GTN homepage.

new feature community building capacity building contributing

What are the most used tools in the GTN?

8 February 2023

Did you ever wonder which was the number one most used tool in the GTN? There is a new page of Top Tools where we list all of the top tools in the GTN, and which tutorials use them. We guessed “upload1”, but it seems like not every author annotates that step explicitly in their tutorial, and of course it doesn’t appear in the workflows which we also scan to create this tool listing.

new feature gtn contributing community

GTN Celebrates Black History Month

2 February 2023

February marks Black History Month in the United States. This year we want to celebrate that by introducing a new theme (Click to Activate), and taking a look at one of the most famous Black figures in Science: Henrietta Lacks whose contribution to science went unremarked and unappreciated for decades while white scientists took credit for advancements built on her cell line.

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screenshot from the data manipulation tutorial

New Tutorial: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

26 January 2023

Food contamination with pathogens are a major burden on our society. Globally, they affect an estimated 600 million people a year and impact socioeconomic development at different levels. These outbreaks are mainly due to Salmonella spp. followed by Campylobacter spp. and Noroviruses.

new tutorial microbiome

New Feature: Prometheus Metrics endpoint

24 January 2023

Prometheus is an increasingly popular monitoring solution whereby sites expose a /metrics endpoint, and then a central Prometheus server can scrape it for data which is then plotted or visualised or alerted upon. We at the GTN are now testing out a prometheus endpoint for our completely static site which we’ll use to expose some maybe useful statistics about the GTN that others can then scrape and display in ways that are useful for them.

new feature gtn contributing

New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic

23 January 2023

The GTN has long struggled with the rigid hierarchy of a single level of classification: topics. All materials had to be organised into a single topic, even when their contents sometimes spanned multiple topics! We added subtopics a while back to help further organise these tutorials, but that still did not solve the issue of needing to collect multiple learn materials in a single location for people to access.

new topic new feature one-health

Content of material available on the GTN and feedback from learners. (A) Evolution of number of topics, tutorials, and contributors over the months between 2017 and 2022. (B) Number and type of tutorials per topics available on the GTN on April 2022. The latest statistics are publicly available from https://training.galaxyproject.org/stats. (C) Type of supporting materials for tutorials per topics available on the GTN on April 2022. (D) Score of the embedded feedback in the tutorials per topics. Three questions are asked in the form: 'How much did you like this tutorial?' (from 1 (bad) to 5 (great)), 'What did you like?', 'What could be improved?'. The latest feedback results are publicly available from https://training.galaxyproject.org/feedback.

New GTN paper: "Galaxy Training: A powerful framework for teaching!"

10 January 2023

Our new paper about the Galaxy Training Network has been published this week in Plos Computational Biology: “Galaxy Training: A powerful framework for teaching!”

paper contributing

Heatmap with columns of cell types vs rows of inferred and actual cell type proportions for A and B samples. Cell colours are similar between actual and inferred.

New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation!

29 November 2022

The still new and shiny single-cell analysis topic now boasts a deconvolution tutorial suite! What does deconvolution do you ask? Well, in this context, it infers cell proportions from bulk RNA-seq data. You heard that correctly - instead of expensive new single-cell experiments, you can re-analyse old bulk RNA-seq data and estimate cell proportions. All you need is a reasonably good single cell dataset to use as a reference and you’re good to go! The tutorial suite shows you how to build your reference from publicly available single cell data, and apply analysis to some publicly available bulk RNA-seq data.

new tutorial single-cell transcriptomics

Pretty dots of different colours combined into two cell cluster plots on the sides. In the middle, a split violin plot showing the expression of unknown genes in blue on one side and the expression of the genes in an opposing sample in orange alongside. Snuck in between these three important plots is a PhD comic of data showing no trend, with the chat box “Hmm… I think there’s a clear trend happening here.”

New Topic: Single Cell Analysis!

18 November 2022

Single-cell analysis now has it’s own topic! These tutorials were previously part of the transcriptomics topic, but due to the amazing efforts by Wendi Bacon, Mehmet Tekmanand others, we now have so many single-cell analysis tutorials that they deserve their own dedicated topic! From introductory slides and practicals, to case study tutorials generating cell clusters and trajectories from raw sequencing files, and even a growing subtopic of smaller tips and tricks for adapting analysis to user needs, the single cell topic either has what you need or is working on it. Come learn or get involved!

new topic single-cell new feature

screenshot from the data manipulation tutorial

New Tutorial: Data Manipulation

11 September 2022

Many analyses in Galaxy require small data manipulations in between tools as a sort of “glue” between analysis steps. For example, you may need to change the file format, re-order columns in a table, replace certain values, or perform some filtering operation, before you can proceed to the next step of your analysis. Galaxy offers a wide range of tools that can perform such generic data manipulation tasks, and mastering these types of operations in Galaxy can help you streamline your analysis and get the most out of Galaxy.

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Access the workflow report from the invocations menu

New Tutorial: Workflow Reports

2 June 2022

Workflow reports are a great Galaxy feature that enable you to define summary reports for any workflow to display the most important results in a single view. This tutorial will guide you through the basics of viewing, customizing, and sharing such workflow reports!

new tutorial Galaxy Tips & Tricks galaxy-interface

GTN Metadata Schemas

20 May 2022

Within the GTN we have had schemas for the various metadata we keep for a long time. It helps us automatically check community contributions to ensure they conform to all of the GTN standards, and will work correctly in our environment.

new feature contributing

Gif showing a user switching between two branches of a tutorial

New Tutorial Feature: Choose Your Own Tutorial

12 April 2022

It has been a long discussed feature within the GTN Tutorial Author Community: how can we provide trainees with choice in their tutorials, and how can we as trainers not duplicate large tutorials just to show a slightly different path at one point?

gtn infrastructure new feature tutorial authors contributing

Assembly of vertebrate genomes

New Tutorial: VGP assembly pipeline

14 March 2022

We are proud to announce that, as result of the collaboration with the Vertebrate Genomes Project (VGP), a new training describing the VGP assembly pipeline is now available in the Galaxy Training Network. The Vertebrate Genomes Project aims to generate high-quality, near-error-free, gap-free, chromosome-level, haplotype-phased, annotated reference genome assemblies for every vertebrate species.

new tutorial assembly pacbio vgp

Image showing content from a tutorial, rendered as an rmarkdown html via knitting. A table of contents appears on the left, and code and outputs on the right.

New Feature: Automatic RMarkdown

28 January 2022

Further building on the work in the automatic Jupyter Notebook, we’ve now re-written the Jupyter export to be faster, and more importantly added support for R and RMarkdown! Check out an example material. Here we take the content of the tutorial, written like normal GTN markdown, and we automatically convert it to Jupyter Notebooks and now RMarkdown documents! Check out the documentation on how to setup your tutorials to support this.

gtn infrastructure new feature contributing

GTN Smörgåsbord 2: Tapas Edition

14 December 2021

This is an external post, please follow the link to read it.

event contributing teaching

Support for annotating Funding Agencies

14 December 2021

The Galaxy Training Network will now support annotating Funding Agencies on training materials. This is part of our ongoing effort to better annotate how people are contributing to the GTN and recognise all of the sources of contribution.

new-feature contributing

Screenshot of a Funannotate annotation displayed with JBrowse, within Galaxy.

New Tutorials: PacBio data QC and Genome Assembly, and Genome Annotation with Funannotate

1 December 2021

We have just finished a new collection of training material for genome assembly and annotation! You now have access to slides and tutorials, focused on the complete analysis of the genome of a fungus species (Mucor mucedo).

new tutorial assembly genome-annotation

New FAQs: How does the GTN stay FAIR and Collaborative

1 December 2021

The GTN does a lot of work to adhere to the best practices for FAIR training materials as set out in Garcia et al. 2020 and a lot of this work is behind-the-scenes or automatic from the infrastructure we provide, and we wanted to highlight that for educators and organisers who want to use GTN materials. This is one of the ways the GTN works to makes itself a fantastic platform training. Find out how contributing simple markdown tutorials can result in fantastically FAIR training.

faq fair contributing

Screenshot of the GTN Video Library Home page

New Feature: GTN Video Library

23 November 2021

After runnning a number of virtual training events this year (e.g. Smörgåsbord, GCC2021), we now have a large collection of training videos around the GTN materials, created by this community.

gtn infrastructure new feature contributing

Image showing an OpenAPI / Swagger UI to the training material API featuring several APIs like topics, tutorials, contributors, and a couple internal APIs. At the bottom are a couple of data models.

New Feature: GTN API with OpenAPI 3 specification

10 November 2021

As part of the work for the Gallantries Grant, we wanted to access some of the data from the GTN in a more accessible, API based way. We are working on building a Video Library based on the wild success of our Smörgåsbord and GCC2021 events and to support that we wanted to start pulling in data from the GTN to save course authors time and effort when designing their asynchronous courses.

gtn infrastructure new feature contributing

Attention Contributors: GTN Performance Enhancements

12 October 2021

Are you one of our amazing GTN Contributors? Were you ever bothered by how slow it was to build the site locally? This is now fixed completely! We have replaced one of the slowest steps of the GTN’s build process and rewritten it ourselves to be more performant.

authors developers performance contributing

New Topic: Data Science Survival Kit

12 October 2021

As part of our work under the Gallantries Grant we are establishing a new topic within the GTN specifically focused on Data Science skills. This topic will include tutorials covering things such as:

gtn infrastructure new topic data-science

Adversitement for the survey. Written: Got a minute? Did you use Galaxy for training / teaching? Have your say... Take our survey. We appreciate your feedback. Logos: Galaxy Project and Galaxy Training Network

Got a minute? Take our survey about Galaxy for training and have your say!

29 September 2021

Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.

feedback contributing

Image comparing Markdown, GTN materials, and new Jupyter Notebook output

New Feature: Automatic Jupyter Notebooks

24 September 2021

As part of the work for the Gallantries Grant, we found ourselves wanting to teach a number of non-Galaxy tutorials on topics such as Python, Bash, SQL, and Git. Writing the tutorials was always a bit awkward as you would spend a lot of time writing code blocks that would be copied and pasted by students into a terminal. We thought we could do better than that, so we decided we would try to convert these to Jupyter Notebooks where the students could read the training materials and simultaneously execute the code cells directly there with the text! This worked fantastically and now we’ve built this feature into the GTN to make it easier to run all of the coding tutorials.

gtn infrastructure new feature contributing

Screenshot of the top of the feedback page with the titles and 2 graphs: the cumulative number of feedback answers over month for all topics, and a barplot with number of answers for different scores

New Feature: a feedback page to aggregate and display feedback answers

28 July 2021

As you have probably already seen, a feedback form is embedded on the bottom of each tutorial.

new feature contributing

Accessibility Improvements

27 July 2021

One of our community members suggested on twitter that we support alternative formats for accessing our JavaScript based slides, as this can be difficult for users using screen readers. We’ve now added support for “plain text slides”, where we render the slide decks as a single long document.

new feature contributing

Analysis flow in the 'Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data' tutorial. It teaches how to obtain, run and combine workflows appropriately for 4 different types of input data. Image adapted from covid19.galaxyproject.org

New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

30 June 2021

Effectively monitoring global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.

new tutorial variant-analysis covid-19 one-health

Screenshot of Volcano Plot customised in R. Significant genes had their colour changed to red, and points and labels were made smaller.

New Tutorial: Visualization of RNA-Seq results with Volcano Plot in R

26 June 2021

The Volcano plot tutorial introduced volcano plots and showed how they can be easily generated with the Galaxy Volcano plot tool. This new tutorial shows how you can customise a plot using the R script output from the tool and RStudio in Galaxy. A short video for the tutorial is also available on YouTube, created for the GCC2021 Training week. Happy plotting!

new tutorial visualisation transcriptomics

Screenshot of the GitPod workspace. A file browser pane on the left, terminal on the bottom, text editor in the middle, and preview of the rendered GTN website on the right.

New Tutorial: GitPod for contributing to the GTN

25 June 2021

Want to contribute to the GTN without installing anything on your own computer? GitPod provides an online workspace for editing the GTN tutorials, and showing a live preview of the GTN website with your changes. This tutorial shows you how to set up GitPod, how to use it to get a live preview of the GTN website, and how to save any changes you make back to your GitHub fork. This makes it easier than ever to contribute to the GTN!

new tutorial contributing

Screenshot of Apollo embedded within the Galaxy Europe interface, Apollo shows a couple of gene tracks.

New Tutorial: Genome Annotation with Apollo

4 June 2021

After two years, the Galaxy Genome Annotation team has finally finished their much awaited tutorial on doing Genome Annotation in Galaxy! Genome annotation is a time consuming and largely manual process as it requires the synthesis of a significant amount of varied information to make inferences, a process tha cannot be accomplished without an interactive editor. To support this, Apollo was deployed on UseGalaxy.eu. Over the past two years the GGA project has pushed forward apollo and tooling around it, and it finally culminates in this look at how to annotated your genomes in Apollo.

new tutorial genome-annotation

Oh no, it changed! Quick, to the archive menu.

1 June 2021

Did you ever start teaching a GTN tutorial, only to realise something changed recently? Oh no! A while ago the GTN created an Archive to address just this concern. On every tag, we’d build a copy of the website which we would place online and never touch again. This way we’d have permanent online copies so that if someone needed to go back to an older version of the GTN, they could.

new feature contributing

Contributing to BioBlend as a developer

25 May 2021

The first of the developer tutorials for GCC2021 is live, first time contributor @gtn:rikeshi has produced a fantastic tutorial covering how to develop new functions in BioBlend for new APIs in Galaxy. Many thanks to @gtn:simonbray for editing!

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New Feature: Easy Abbreviation

25 May 2021

Thanks to the great tutorial developed by first time contributor @gtn:rikeshi and edited by @gtn:simonbray, we noticed that they defined a number of abbreviations and re-used those throughout their tutorial.

new feature contributing

Hello in many languages

¿Hablas español?: The first curated tutorial in Spanish!

20 May 2021

¡El primer tutorial en español ya está disponible! Galaxy siempre ha tenido tutoriales traducidos automáticamente mediante Google-Translate, ahora nos estamos embarcando en un nuevo proyecto para estudiar la experiencia de aprendizaje con tutoriales en bioinformática traducidos por humanos. Nuestro objetivo es crear un paquete de tutoriales para el análisis de datos single-cell (célula única) en primera instancia, con el fin de estudiar su uso y utilidad en un taller para hablantes nativos de español. Agradecemos enormemente a las nuevas participantes @gtn:pclo y @gtn:ales-ibt (EMBL-EBI) así como a las miembros existentes de GTN @gtn:beatrizserrano (University of Freiburg), @gtn:shiltemann & @gtn:hexylena (Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a @gtn:nomadscientist (The Open University/EBI) como líder de proyecto.

new tutorial español introduction

Biosynthesis of miRNA in plants

New Tutorials: Whole transcriptome analysis of Arabidopsis thaliana

10 April 2021

Plant lovers are in luck! A new tutorial on this fascinating kingdom has been added to the GTN. It details the necessary steps to identify potential targets of brassinosteroid-induced miRNAs. Brassinosteroids are phytohormones that have the ability to stimulate plant growth and confer resistance against abiotic and biotic stresses. These characteristics have led to great interest in the field of biotechnology due to its potential for increasing agricultural productivity.

new tutorial transcriptomics plants mirna

Example of video player mimicking youtube's interface with a video at the top, a transcript at the bottom left, and suggested videos at the bottom right.

New Feature: Video Player

6 April 2021

One of our contributors (@gtn:mtekman) found himself wanting to link to a specific time point in a video. We said “Wow, what a fantastic idea!” and then we implemented it. To support that we developed a very simple standalone video player page where you can view the GTN videos and browse through our catalog. It features the full transcript on the left, some suggested videos on the right, and a very standard <video> player.

gtn infrastructure video new feature contributing

Arabidopsis clusters with trajectory from meristematic cells towards trichoblasts

New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy

30 March 2021

Single cell RNA-seq analysis is a cornerstone of developmental research and provides a great level of detail in understanding the underlying dynamic processes within tissues. In the context of plants, this highlights some of the key differentiation pathways that root cells undergo.

new tutorial single-cell plant

Assembly visualisation from the Bandage tool

New Tutorials: Genome assembly of a MRSA genome

24 March 2021

Two new assembly tutorials have been added to the GTN! These tutorials walk you through the process of assembling MRSA strains from real-world datasets. MRSA stands for “Methicillin- resistant Staphylococcus aureus, it is resistance to several antibiotics and is a common source of hospital-acquired infections and outbreaks. In this tutorial you will assess the quality of your data, perform an assembly and assess its quality, analyze your data for the presence of antimicrobial resistance (AMR) genes, and annotate the genome using Prokka and JBrowse.

new tutorial assembly mrsa amr nanopore illumina

New Feature: FAQs

24 March 2021

Snippets have received an major overhaul! Snippets/FAQs are small reusable bits of training, often answering a single question. In addition to the general Galaxy snippets, we now also support topic-level and tutorial-level FAQs. This will allow contributors to add common questions and answers to their tutorials, which not only can be included in the tutorial text itself, but are also used to autogenerate an FAQ page for the tutorial or topic listing all common questions (and answers).This will be useful both to participants following tutorials via self-study, and also to instructors preparing for a training event.

gtn infrastructure contributors instructors new feature contributing

Video of green coloured cells dividing on a dark background.

New Tutorial: Object tracking using CellProfiler

18 March 2021

Most biological processes are dynamic and observing them over time can provide valuable insights. Combining fluorescent markers with time-lapse imaging is a common approach to collect data on dynamic cellular processes such as cell division. However, automated time-lapse imaging can produce large amounts of data that can be challenging to process. One of these challenges is the tracking of individual objects as it is often impossible to manually follow a large number of objects over many time points.

new tutorial imaging

Next GTN CoFest May 20, 2021

18 March 2021

Every 3 months we organise one day dedicated to the GTN community! Thursday, May 20th is the next GTN CoFest. We will be working on the training materials, have discussions with the global Galaxy traning community. Do you teach with Galaxy? Want to learn how to add your tutorial to the GTN? New to the community and just want to learn more? Everybody is welcome!

cofest contributing

Galaxy Community Conference 2021

18 March 2021

This is an external post, please follow the link to read it.

event

Wordcloud of emoji with them in different sizes based on frequency

Report on the GTN Smörgåsbord event

17 March 2021

The GTN instructors community has just run the largest-ever Galaxy training event: “the GTN Smörgåsbord: A Global Galaxy Course”, co-organized with the Gallantries and the CINECA project and the Galaxy Training Network.

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Galaxy 21.01 released!

17 March 2021

The Galaxy Team is pleased to announce the release of Galaxy 21.01! Workflows are the absolute ✨star✨, followed closely by the new Remote Files interface and much more.

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New Feature: Automatic Slides-to-video conversion

16 March 2021

This past year has been a struggle for all of us, but one task has become apparent as one of the most time consuming portions of course preparation during a pandemic: Video Production.

new feature videos gtn pandemic remote-teaching contributing

Galaxy Admin Training Success

1 March 2021

The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event.

admin gat event pandemic remote-teaching